Contacts of the helix formed by residues 101 - 115 (chain A) in PDB entry 1FXT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.7 8.5 - - - +
9A LYS* 6.3 0.9 - - + -
10A GLU* 3.7 20.4 - - + +
62A TYR* 4.7 0.2 - - - -
96A TRP* 5.6 0.2 - - - -
99A VAL 3.6 6.7 + - - +
100A ILE* 1.3 75.8 - - - +
102A LEU* 1.3 58.1 + - - +
103A LYS* 4.1 9.6 - - - +
104A SER* 3.0 26.3 + - - -
105A ALA* 2.9 25.0 + - - +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.7 24.2 - - + -
10A GLU* 2.9 21.2 + - - +
22A ILE* 4.9 0.4 - - - +
24A LEU* 4.1 24.9 - - + -
35A LEU* 3.8 19.7 - - + -
56A ILE* 4.3 20.9 - - + -
58A VAL* 4.0 21.8 - - + -
62A TYR* 3.8 6.3 - - - +
67A PRO* 4.2 19.5 - - + -
69A MET* 4.6 0.7 - - + -
96A TRP* 5.5 1.3 - - + -
100A ILE 4.0 0.4 + - - -
101A THR* 1.3 69.9 - - - +
103A LYS* 1.3 56.7 + - - +
105A ALA* 4.0 12.3 - - + -
106A LEU* 3.1 39.3 + - + +
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 4.7 6.2 - - + +
13A ALA* 2.8 40.9 + - + +
14A VAL* 3.8 28.5 - - + +
17A ASP* 2.7 33.4 + - - +
20A ALA* 3.6 23.6 - - + -
22A ILE* 4.4 8.8 - - + +
24A LEU* 4.9 0.2 - - - +
101A THR* 4.1 11.1 - - - +
102A LEU* 1.3 74.9 - - - +
104A SER* 1.3 56.3 + - - +
107A ILE* 3.3 34.2 + - + +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 4.4 12.6 - - - +
101A THR* 3.0 28.7 + - - -
103A LYS* 1.3 70.5 - - - +
105A ALA* 1.3 57.5 + - - -
106A LEU 3.7 0.2 - - - -
107A ILE* 3.6 1.7 + - - -
108A SER* 3.0 13.2 + - - -
6B LYS* 2.9 45.8 + - - +
7B THR 3.6 14.6 + - - -
8B LEU* 4.7 2.4 - - - +
10B GLY 5.8 1.5 + - - -
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A MET* 4.0 14.1 - - + +
92A LEU* 3.8 23.6 - - + +
96A TRP* 4.7 3.4 - - + -
100A ILE* 4.4 11.8 - - + +
101A THR 2.9 17.8 + - - +
102A LEU* 3.3 15.4 + - + +
104A SER* 1.3 69.7 - - - +
106A LEU* 1.3 64.2 + - - +
108A SER* 3.3 22.2 + - - -
109A LEU* 3.3 11.8 + - - +
8B LEU* 5.8 0.4 - - - -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.6 25.1 - - + -
24A LEU* 4.1 11.0 - - + -
37A GLY* 3.3 32.8 - - - +
38A THR 4.4 0.4 - - - +
39A PHE* 3.6 16.7 - - + -
54A VAL* 4.0 19.3 - - + -
56A ILE* 3.9 19.5 - - + -
69A MET* 4.1 11.2 - - + -
102A LEU* 3.1 42.8 + - + +
105A ALA* 1.3 68.6 - - - +
107A ILE* 1.4 60.1 + - - +
109A LEU* 3.4 14.7 + - + +
110A GLN* 3.1 23.6 + - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.5 39.5 - - + +
22A ILE* 4.0 7.2 - - + -
103A LYS* 3.3 23.8 + - + +
104A SER* 3.6 5.0 + - - +
105A ALA 3.5 0.4 - - - -
106A LEU* 1.4 71.3 - - - +
108A SER* 1.4 59.3 + - - +
110A GLN* 3.6 23.4 - - - +
111A ALA* 3.1 27.2 + - - +
6B LYS* 3.9 12.5 + - - +
68B HIS* 3.6 36.1 - - + +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.6 12.4 - - - +
92A LEU* 4.7 6.5 - - - -
104A SER 3.0 10.9 + - - -
105A ALA* 3.3 15.0 + - - -
107A ILE* 1.4 74.6 - - - +
109A LEU* 1.3 57.1 + - - +
111A ALA* 3.6 5.5 + - - +
112A LEU* 2.9 29.6 + - - +
6B LYS* 3.6 4.1 - - - +
8B LEU* 3.2 43.7 - - - +
70B VAL* 4.1 6.8 - - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.5 17.9 - - + -
54A VAL* 3.9 23.3 - - + -
69A MET* 3.7 15.5 - - - -
71A PHE* 4.3 2.0 - - + -
80A ILE* 4.4 7.0 - - + +
87A ILE* 3.7 43.1 - - + -
92A LEU* 3.8 21.5 - - + -
105A ALA 3.3 10.3 + - - +
106A LEU* 3.4 12.9 + - + +
108A SER* 1.3 71.0 - - - +
110A GLN* 1.3 59.7 + - - +
112A LEU* 3.6 15.0 - - + +
113A LEU* 3.0 34.1 + - - +
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Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA 5.0 0.7 - - - +
21A HIS* 3.5 32.8 + - - +
22A ILE* 5.6 0.4 - - - +
39A PHE* 3.7 19.8 - - + +
40A LEU 3.0 30.9 + - - +
41A GLY 5.3 0.2 - - - -
42A PRO* 3.1 23.3 - - + +
106A LEU 3.1 13.0 + - - +
107A ILE* 3.6 34.5 - - - +
109A LEU* 1.3 75.3 - - - +
111A ALA* 1.3 56.0 + - - +
113A LEU 3.5 0.2 + - - -
114A GLN* 3.0 24.9 + - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 3.1 19.0 + - + +
108A SER* 3.9 0.9 - - - +
110A GLN* 1.3 71.1 - - - +
112A LEU* 1.3 60.4 + - - +
114A GLN* 3.7 13.9 + - - +
6B LYS* 6.2 0.2 - - - +
42B ARG* 2.9 17.8 + - - -
44B ILE* 3.6 28.6 - - + +
68B HIS* 4.4 14.8 - - + -
70B VAL* 3.6 24.2 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A HIS* 3.3 19.4 + - - +
79A ASN* 3.4 41.0 - - + +
80A ILE* 4.1 18.2 - - + -
87A ILE* 4.5 1.1 - - + -
88A CYS 4.4 9.2 - - - +
89A LEU* 4.2 29.4 - - + -
108A SER 2.9 21.2 + - - +
109A LEU* 3.4 18.1 + - + +
111A ALA* 1.3 71.1 - - - +
113A LEU* 1.3 58.7 + - - +
115A SER 4.2 1.4 - - - +
116A PRO* 4.5 0.2 - - - +
42B ARG* 3.1 38.2 + - - +
70B VAL* 4.3 6.3 - - + +
72B ARG* 5.4 2.5 - - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.7 22.7 - - + -
42A PRO* 4.1 3.8 - - + -
45A THR* 3.9 0.7 - - - +
47A TYR* 3.3 36.5 - - + -
52A PHE* 3.6 34.5 - - + -
71A PHE* 5.2 0.2 - - + -
75A VAL* 3.7 16.2 - - + -
77A HIS* 3.5 31.9 - - + +
80A ILE* 3.6 19.5 - - + -
109A LEU 3.0 20.1 + - - +
110A GLN 3.8 3.8 - - - +
112A LEU* 1.3 72.0 - - - +
114A GLN* 1.3 63.9 + - - +
115A SER 3.1 1.7 + - - -
116A PRO* 3.6 10.0 - - - +
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 3.6 24.6 - - + +
43A PRO* 3.2 25.2 + - - +
45A THR* 3.1 40.3 + - - +
110A GLN 3.0 19.6 + - - +
111A ALA* 3.9 8.7 - - - +
112A LEU 3.6 1.2 - - - -
113A LEU* 1.3 70.6 - - - +
115A SER* 1.3 63.2 + - - +
116A PRO* 4.2 1.1 - - - +
44B ILE* 3.8 24.2 - - + -
46B ALA* 4.2 4.3 - - - +
47B GLY* 3.1 31.5 + - - +
48B LYS 4.3 5.8 - - - +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU 3.1 1.0 + - - -
114A GLN* 1.3 82.8 + - - +
116A PRO* 1.4 65.2 - - - +
117A GLU* 4.0 2.0 - - - +
42B ARG* 2.8 37.3 + - - +
44B ILE* 4.3 3.1 - - - +
47B GLY 4.7 1.0 + - - -
48B LYS* 3.7 7.1 - - - -
49B GLN* 3.4 43.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il